Gene Gene information from NCBI Gene database.
Entrez ID 1184
Gene name Chloride voltage-gated channel 5
Gene symbol CLCN5
Synonyms (NCBI Gene)
CLC5CLCK2ClC-5DENT1DENTSNPHL1NPHL2XLRHXRNhCIC-K2
Chromosome X
Chromosome location Xp11.23
Summary This gene encodes a member of the ClC family of chloride ion channels and ion transporters. The encoded protein is primarily localized to endosomal membranes and may function to facilitate albumin uptake by the renal proximal tubule. Mutations in this gen
SNPs SNP information provided by dbSNP.
41
SNP ID Visualize variation Clinical significance Consequence
rs151340620 G>A Pathogenic Stop gained, genic downstream transcript variant, coding sequence variant
rs151340621 C>A,T Pathogenic Synonymous variant, stop gained, genic downstream transcript variant, coding sequence variant
rs151340622 T>G Pathogenic Missense variant, genic downstream transcript variant, coding sequence variant
rs151340623 T>C Pathogenic Missense variant, genic downstream transcript variant, coding sequence variant
rs151340624 C>T Pathogenic, uncertain-significance Stop gained, genic downstream transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
426
miRTarBase ID miRNA Experiments Reference
MIRT030774 hsa-miR-21-5p Microarray 18591254
MIRT479205 hsa-miR-302f PAR-CLIP 20371350
MIRT479204 hsa-miR-6808-5p PAR-CLIP 20371350
MIRT479202 hsa-miR-6893-5p PAR-CLIP 20371350
MIRT479203 hsa-miR-940 PAR-CLIP 20371350
Transcription factors Transcription factors information provided by TRRUST V2 database.
1
Transcription factor Regulation Reference
TFAP4 Unknown 15086899
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
38
GO ID Ontology Definition Evidence Reference
GO:0000139 Component Golgi membrane IEA
GO:0000166 Function Nucleotide binding IEA
GO:0003014 Process Renal system process IMP 8559248
GO:0005247 Function Voltage-gated chloride channel activity IBA
GO:0005247 Function Voltage-gated chloride channel activity IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300008 2023 ENSG00000171365
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P51795
Protein name H(+)/Cl(-) exchange transporter 5 (Chloride channel protein 5) (ClC-5) (Chloride transporter ClC-5)
Protein function Proton-coupled chloride transporter. Functions as antiport system and exchanges chloride ions against protons (PubMed:20466723). Important for normal acidification of the endosome lumen. May play an important role in renal tubular function. The
PDB 2J9L , 2JA3
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00654 Voltage_CLC 149 551 Voltage gated chloride channel Family
PF00571 CBS 582 646 CBS domain Domain
PF00571 CBS 679 734 CBS domain Domain
Tissue specificity TISSUE SPECIFICITY: Kidney. Moderately expressed in aortic vascular smooth muscle and endothelial cells, and at a slightly higher level in the coronary vascular smooth muscle. {ECO:0000269|PubMed:10198195}.
Sequence
MAMWQGAMDNRGFQQGSFSSFQNSSSDEDLMDIPATAMDFSMRDDVPPLDREVGEDKSYN
GGGIGSSNRIMDFLEEPIPGVGTYDDFNTIDWVREKSRDRDRHREITNKSKESTWALIHS
VSDAFSGWLLMLLIGLLSGSLAGLIDISAHWMTDLKEGICTGGFWFNHEHCCWNSEHVTF
EERDKCPEWNSWSQLIISTDEGAFAYIVNYFMYVLWALLFAFLAVSLVKVFAPYACGSGI
PEIKTILSGFIIRGYLGKWTLVIKTITLVLAVSSGLSLGKEGPLVHVACCCGNILCHCFN
KYRKNEAKRREVLSAAAAAGVSVAFGAPIGGVLFSLEEVSYYFPLKTLWRSFFAALVAAF
TLRSINPFGNSRLVLFYVEFHTPWHLFELVPFILLGIFGGLWGALFIRTNIAWCRKRKTT
QLGKYPVIEVLVVTAITAILAFPNEYTRMSTSELISELFNDCGLLDSSKLCDYENRFNTS
KGGELPDRPAGVGVYSAMWQLALTLILKIVITIFTFGMKIPSGLFIPSMAVGAIAGRLLG
VGMEQLAYYHQ
EWTVFNSWCSQGADCITPGLYAMVGAAACLGGVTRMTVSLVVIMFELTG
GLEYIVPLMAAAMTSKWVADALGREGIYDAHIRLNGYPFLEAKEEF
AHKTLAMDVMKPRR
NDPLLTVLTQDSMTVEDVETIISETTYSGFPVVVSRESQRLVGFVLRRDLIISIENARKK
QDGVVSTSIIYFTE
HSPPLPPYTPPTLKLRNILDLSPFTVTDLTPMEIVVDIFRKLGLRQ
CLVTHNGRLLGIITKKDVLKHIAQMANQDPDSILFN
Sequence length 816
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Neutrophil extracellular trap formation   Stimuli-sensing channels
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
26
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
CLCN5-related disorder Likely pathogenic; Pathogenic rs797044808, rs151340626, rs2519444688, rs2519445104 RCV003417691
RCV003398487
RCV003397449
RCV003393020
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dent disease Pathogenic rs797044813 RCV003401037
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dent disease type 1 Pathogenic; Likely pathogenic rs2147594126, rs2147582103, rs2147594243, rs782720805, rs2147605760, rs2147596542, rs2147606263, rs2519435022, rs797044808, rs797044810, rs797044811, rs797044812, rs797044813, rs797044814, rs797044815
View all (44 more)
RCV001580334
RCV001580335
RCV001814743
RCV001843320
RCV001849668
View all (54 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Familial X-linked hypophosphatemic vitamin D refractory rickets Likely pathogenic; Pathogenic rs797044808 RCV004546452
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign; Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bethlem myopathy 1A Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DENT DISEASE 1 CTD, Disgenet, HPO
CTD, Disgenet, HPO
CTD, Disgenet, HPO
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DENTS DISEASE Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adult Rickets Rickets HPO_DG
★☆☆☆☆
Found in Text Mining only
Alport Syndrome Alport Syndrome BEFREE 31364286
★☆☆☆☆
Found in Text Mining only
Bartter Disease Bartter syndrome BEFREE 30405442
★☆☆☆☆
Found in Text Mining only
Cartilaginous exostosis Osteochondroma BEFREE 25792359
★☆☆☆☆
Found in Text Mining only
Cholangiocarcinoma Cholangiocarcinoma Pubtator 35651328 Associate
★☆☆☆☆
Found in Text Mining only
Chronic kidney disease stage 5 Kidney Disease BEFREE 16247550
★☆☆☆☆
Found in Text Mining only
Chronic Kidney Diseases Kidney Disease BEFREE 27699523, 31054069
★☆☆☆☆
Found in Text Mining only
Chronic Kidney Diseases Kidney Disease HPO_DG
★☆☆☆☆
Found in Text Mining only
Chronic Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 25909590
★☆☆☆☆
Found in Text Mining only
Classical Lissencephaly Lissencephaly BEFREE 29338612
★☆☆☆☆
Found in Text Mining only